New legislation comes into effect to tighten document checks across the EU, particularly in countries at the bloc's external borders.
Officials warned this, in addition to systematic checks on all third-country nationals entering the Schengen Zone, was likely to prompt longer queues at frontier checkpoints.
Disgruntled drivers on the Croatian border with Slovenia appeared to confirm the extended waiting time.
“It’s a disaster. I have two disabled people in my car – they need to go to the bathroom, and have nowhere to go,” said one man.
“We waited at the Croatian border for an hour and a half and also at the Slovenian border for an hour and a half – so, three hours altogether. We are waiting with two small children in the car.”
First proposed after the 2015 Paris attacks, the new measures are described as a response to “the growing threat from foreign terrorist fighters.”
While new to some countries, others such as Romania have been conducting thorough border checks for some time.
Alexandra Popescu, a spokesperson for the Romanian Border Police explained the checks.
“If they find that one of these people, or the document the person presented at the border crossing point, appears in the data base with a warning note, that person is invited to the second queue, where the Border Police officers will conduct further detailed verifications. But this procedure will not affect the fluidity of passenger traffic,” she said.
Countries are now required to check all travellers against three databases – Schengen, Interpol and national. Authorities say the average time to carry this out is around two minutes per person.